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help needed processing 4D 13C-HMQC-NOESY-15N-HSQC

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  • Sean Cahill
    Hi, I ran a 4D 13C-HMQC-NOESY-15N-HSQC on a Varian Inova600 using the pulse sequence gChmqcnoesyNhsqc and I am trying to process it up using nmrpipe. Before
    Message 1 of 3 , Jun 5, 2007
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      Hi, I ran a 4D 13C-HMQC-NOESY-15N-HSQC on a Varian Inova600 using the pulse
      sequence gChmqcnoesyNhsqc and I am trying to process it up using nmrpipe.
      Before running the 4D, I ran the 1H-1H, 1H-13C and 1H-15N 2D planes and they
      processed up and look fine using nmrpipe. However, by mistake, the 4D was
      run using an array order of 'phase,phase3,phase2' and I think this might be
      the source of our problem. I have tried various aqORD values (0, 1 and 2) in
      the var2pipe script but the data in the 1H-13C and 1H-15N dimensions are
      messed up (the 1H-1H dimension looks fine). In fact, if I view the aqORD
      options using var2pipe -help, I get the following:

      -aqORD aqOrd [0] Acquisition Order Code.
      0 = 2D d2,phase
      0 = 3D d3,d2,phase2,phase
      0 = 4D d4,d3,d2,phase3,phase2,phase
      1 = 3D d3,d2,phase,phase2
      1 = 4D d4,d3,d2,phase,phase2,phase3
      2 = 4D d3,d2,d4,phase3,phase2,phase

      but none of these options correspond to the order that we acquired the
      dataset with. Is there any hope for us??? Thanks in advance for any help.
      Sean

      ----------------------------------------------------
      Sean Cahill, Structural NMR Resource
      Albert Einstein College of Medicine
      1300 Morris Park Ave, Bronx, NY 10461
    • delaglio@nmrscience.com
      Ok, don t despair ... for cases like this, we have a script called varAdjust.tcl which allows us to re-order the arrangement of real and imaginary data (see
      Message 2 of 3 , Jun 6, 2007
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        Ok, don't despair ... for cases like this, we have a script called
        "varAdjust.tcl" which allows us to re-order the arrangement of real
        and imaginary data (see "varAdjust.tcl -help") ...

        For example, in a varian 3D, the data vectors are grouped in sets of
        4 complex vectors, which are in 2 possible orders:

        phase2,phase:
        1=(y=real, z=real) 2=(y=imag, z=real) 3=(y=real, z=imag) 4=(y=imag, z=imag)

        phase,phase2:
        1=(y=real, z=real) 2=(y=real, z=imag) 3=(y=imag, z=real) 4=(y=imag, z=imag)

        So for example, to convert phase,phase2 data to phase2,phase:

        varAdjust.tcl -order 1 3 2 4 ...

        Quoting Sean Cahill <cahill@...>:

        > Hi, I ran a 4D 13C-HMQC-NOESY-15N-HSQC on a Varian Inova600 using the pulse
        > sequence gChmqcnoesyNhsqc and I am trying to process it up using nmrpipe.
        > Before running the 4D, I ran the 1H-1H, 1H-13C and 1H-15N 2D planes and they
        > processed up and look fine using nmrpipe. However, by mistake, the 4D was
        > run using an array order of 'phase,phase3,phase2' and I think this might be
        > the source of our problem. I have tried various aqORD values (0, 1 and 2) in
        > the var2pipe script but the data in the 1H-13C and 1H-15N dimensions are
        > messed up (the 1H-1H dimension looks fine). In fact, if I view the aqORD
        > options using var2pipe -help, I get the following:
        >
        > -aqORD aqOrd [0] Acquisition Order Code.
        > 0 = 2D d2,phase
        > 0 = 3D d3,d2,phase2,phase
        > 0 = 4D d4,d3,d2,phase3,phase2,phase
        > 1 = 3D d3,d2,phase,phase2
        > 1 = 4D d4,d3,d2,phase,phase2,phase3
        > 2 = 4D d3,d2,d4,phase3,phase2,phase
        >
        > but none of these options correspond to the order that we acquired the
        > dataset with. Is there any hope for us??? Thanks in advance for any help.
        > Sean
        >
        > ----------------------------------------------------
        > Sean Cahill, Structural NMR Resource
        > Albert Einstein College of Medicine
        > 1300 Morris Park Ave, Bronx, NY 10461
        >
        >
        >
      • Sean Cahill
        Thanks Frank! as usual, you re right on - your script worked like a charm and we were able to process up the 4D experiment by first using the command:
        Message 3 of 3 , Jun 7, 2007
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          Thanks Frank! as usual, you're right on - your script worked like a
          charm and we were able to process up the 4D experiment by first using
          the command:

          varAdjust.tcl -order 1 3 2 4 5 7 6 8 -in 4Dnoesy.fid -out
          4Dnoesy.fid.adj
          (to change order of data vectors from phase,phase3,phase2 to
          phase,phase2,phase3)

          and then sending the file 4Dnoesy.fid.adj through our nmrpipe script
          using "-aqORD 1"

          Thanks a million and best regards, Sean

          delaglio@... wrote:
          >
          > Ok, don't despair ... for cases like this, we have a script called
          > "varAdjust.tcl" which allows us to re-order the arrangement of real
          > and imaginary data (see "varAdjust.tcl -help") ...
          >
          > For example, in a varian 3D, the data vectors are grouped in sets of
          > 4 complex vectors, which are in 2 possible orders:
          >
          > phase2,phase:
          > 1=(y=real, z=real) 2=(y=imag, z=real) 3=(y=real, z=imag) 4=(y=imag, z=imag)
          >
          > phase,phase2:
          > 1=(y=real, z=real) 2=(y=real, z=imag) 3=(y=imag, z=real) 4=(y=imag, z=imag)
          >
          > So for example, to convert phase,phase2 data to phase2,phase:
          >
          > varAdjust.tcl -order 1 3 2 4 ...
          >
          > Quoting Sean Cahill <cahill@...>:
          >
          > > Hi, I ran a 4D 13C-HMQC-NOESY-15N-HSQC on a Varian Inova600 using the pulse
          > > sequence gChmqcnoesyNhsqc and I am trying to process it up using nmrpipe.
          > > Before running the 4D, I ran the 1H-1H, 1H-13C and 1H-15N 2D planes and they
          > > processed up and look fine using nmrpipe. However, by mistake, the 4D was
          > > run using an array order of 'phase,phase3,phase2' and I think this might be
          > > the source of our problem. I have tried various aqORD values (0, 1 and 2) in
          > > the var2pipe script but the data in the 1H-13C and 1H-15N dimensions are
          > > messed up (the 1H-1H dimension looks fine). In fact, if I view the aqORD
          > > options using var2pipe -help, I get the following:
          > >
          > > -aqORD aqOrd [0] Acquisition Order Code.
          > > 0 = 2D d2,phase
          > > 0 = 3D d3,d2,phase2,phase
          > > 0 = 4D d4,d3,d2,phase3,phase2,phase
          > > 1 = 3D d3,d2,phase,phase2
          > > 1 = 4D d4,d3,d2,phase,phase2,phase3
          > > 2 = 4D d3,d2,d4,phase3,phase2,phase
          > >
          > > but none of these options correspond to the order that we acquired the
          > > dataset with. Is there any hope for us??? Thanks in advance for any help.
          > > Sean
          > >
          > > ----------------------------------------------------
          > > Sean Cahill, Structural NMR Resource
          > > Albert Einstein College of Medicine
          > > 1300 Morris Park Ave, Bronx, NY 10461
          > >
          > >
          > >
          >
          >
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